Continuing printing with the Anycubic Photon S, some issues seem to be working themselves out.
Caps: the magnet recesses still seem to be undersized, with an internal diameter between 5.0mm and 5.5mm creating a push fit for this component. An internal diameter between 1.0mm and 1.5mm (depth of 2mm, fillet radius 0.2mm at each end) leads to a hole that just opens up.
Nodes: leaving the printer alone during the print (so not using the pause function and ensuring I did not knock it) removed z-wobble issues, using side-cutters removed the pock-marks in the sides of the node, with any bumps removed with sandpaper. Using increasing sandpaper grits should increase the surface quality until it reaches a condition that cannot be differentiated from the rest of the node, without supports.